[2023-06-27 20:06:32,862] [INFO] DFAST_QC pipeline started.
[2023-06-27 20:06:32,863] [INFO] DFAST_QC version: 0.5.7
[2023-06-27 20:06:32,864] [INFO] DQC Reference Directory: /var/lib/cwl/stgd7b888b7-a127-4b23-95b9-7e208935f81a/dqc_reference
[2023-06-27 20:06:35,904] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-27 20:06:35,905] [INFO] Task started: Prodigal
[2023-06-27 20:06:35,905] [INFO] Running command: gunzip -c /var/lib/cwl/stgaaa23a08-5330-4b62-a5da-1510e82d2791/GCA_026552815.1_ASM2655281v1_genomic.fna.gz | prodigal -d GCA_026552815.1_ASM2655281v1_genomic.fna/cds.fna -a GCA_026552815.1_ASM2655281v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-27 20:06:40,295] [INFO] Task succeeded: Prodigal
[2023-06-27 20:06:40,295] [INFO] Task started: HMMsearch
[2023-06-27 20:06:40,295] [INFO] Running command: hmmsearch --tblout GCA_026552815.1_ASM2655281v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd7b888b7-a127-4b23-95b9-7e208935f81a/dqc_reference/reference_markers.hmm GCA_026552815.1_ASM2655281v1_genomic.fna/protein.faa > /dev/null
[2023-06-27 20:06:40,515] [INFO] Task succeeded: HMMsearch
[2023-06-27 20:06:40,517] [WARNING] Found 3/6 markers. [/var/lib/cwl/stgaaa23a08-5330-4b62-a5da-1510e82d2791/GCA_026552815.1_ASM2655281v1_genomic.fna.gz]
[2023-06-27 20:06:40,546] [INFO] Query marker FASTA was written to GCA_026552815.1_ASM2655281v1_genomic.fna/markers.fasta
[2023-06-27 20:06:40,546] [INFO] Task started: Blastn
[2023-06-27 20:06:40,546] [INFO] Running command: blastn -query GCA_026552815.1_ASM2655281v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd7b888b7-a127-4b23-95b9-7e208935f81a/dqc_reference/reference_markers.fasta -out GCA_026552815.1_ASM2655281v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-27 20:06:41,040] [INFO] Task succeeded: Blastn
[2023-06-27 20:06:41,044] [INFO] Selected 7 target genomes.
[2023-06-27 20:06:41,044] [INFO] Target genome list was writen to GCA_026552815.1_ASM2655281v1_genomic.fna/target_genomes.txt
[2023-06-27 20:06:41,045] [INFO] Task started: fastANI
[2023-06-27 20:06:41,045] [INFO] Running command: fastANI --query /var/lib/cwl/stgaaa23a08-5330-4b62-a5da-1510e82d2791/GCA_026552815.1_ASM2655281v1_genomic.fna.gz --refList GCA_026552815.1_ASM2655281v1_genomic.fna/target_genomes.txt --output GCA_026552815.1_ASM2655281v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-27 20:06:43,146] [INFO] Task succeeded: fastANI
[2023-06-27 20:06:43,147] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd7b888b7-a127-4b23-95b9-7e208935f81a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-27 20:06:43,147] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd7b888b7-a127-4b23-95b9-7e208935f81a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-27 20:06:43,152] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-27 20:06:43,153] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-27 20:06:43,153] [INFO] DFAST Taxonomy check final result
--------------------------------------------------------------------------------
organism_name	strain	accession	taxid	species_taxid	relation_to_type	validated	ani	matched_fragments	total_fragments	ani_threshold	status
--------------------------------------------------------------------------------
[2023-06-27 20:06:43,156] [INFO] DFAST Taxonomy check result was written to GCA_026552815.1_ASM2655281v1_genomic.fna/tc_result.tsv
[2023-06-27 20:06:43,157] [INFO] ===== Taxonomy check completed =====
[2023-06-27 20:06:43,157] [INFO] ===== Start completeness check using CheckM =====
[2023-06-27 20:06:43,158] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd7b888b7-a127-4b23-95b9-7e208935f81a/dqc_reference/checkm_data
[2023-06-27 20:06:43,165] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-27 20:06:43,189] [INFO] Task started: CheckM
[2023-06-27 20:06:43,189] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_026552815.1_ASM2655281v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_026552815.1_ASM2655281v1_genomic.fna/checkm_input GCA_026552815.1_ASM2655281v1_genomic.fna/checkm_result
[2023-06-27 20:07:03,936] [INFO] Task succeeded: CheckM
[2023-06-27 20:07:03,938] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-27 20:07:03,973] [INFO] ===== Completeness check finished =====
[2023-06-27 20:07:03,974] [INFO] ===== Start GTDB Search =====
[2023-06-27 20:07:03,974] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_026552815.1_ASM2655281v1_genomic.fna/markers.fasta)
[2023-06-27 20:07:03,975] [INFO] Task started: Blastn
[2023-06-27 20:07:03,975] [INFO] Running command: blastn -query GCA_026552815.1_ASM2655281v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd7b888b7-a127-4b23-95b9-7e208935f81a/dqc_reference/reference_markers_gtdb.fasta -out GCA_026552815.1_ASM2655281v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-27 20:07:04,445] [INFO] Task succeeded: Blastn
[2023-06-27 20:07:04,449] [INFO] Selected 8 target genomes.
[2023-06-27 20:07:04,449] [INFO] Target genome list was writen to GCA_026552815.1_ASM2655281v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-27 20:07:04,454] [INFO] Task started: fastANI
[2023-06-27 20:07:04,455] [INFO] Running command: fastANI --query /var/lib/cwl/stgaaa23a08-5330-4b62-a5da-1510e82d2791/GCA_026552815.1_ASM2655281v1_genomic.fna.gz --refList GCA_026552815.1_ASM2655281v1_genomic.fna/target_genomes_gtdb.txt --output GCA_026552815.1_ASM2655281v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-27 20:07:07,936] [INFO] Task succeeded: fastANI
[2023-06-27 20:07:07,950] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-27 20:07:07,951] [INFO] GTDB search result
--------------------------------------------------------------------------------
accession	gtdb_species	ani	matched_fragments	total_fragments	gtdb_taxonomy	ani_circumscription_radius	mean_intra_species_ani	min_intra_species_ani	mean_intra_species_af	min_intra_species_af	num_clustered_genomes	status
GCA_002839545.1	s__Methanoperedens_A sp002839545	100.0	590	599	d__Archaea;p__Halobacteriota;c__Methanosarcinia;o__Methanosarcinales;f__Methanoperedenaceae;g__Methanoperedens_A	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_014859785.1	s__Methanoperedens_A sp014859785	84.5534	338	599	d__Archaea;p__Halobacteriota;c__Methanosarcinia;o__Methanosarcinales;f__Methanoperedenaceae;g__Methanoperedens_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012026835.1	s__Methanoperedens sp012026835	76.7614	85	599	d__Archaea;p__Halobacteriota;c__Methanosarcinia;o__Methanosarcinales;f__Methanoperedenaceae;g__Methanoperedens	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003104905.1	s__Methanoperedens sp003104905	76.595	65	599	d__Archaea;p__Halobacteriota;c__Methanosarcinia;o__Methanosarcinales;f__Methanoperedenaceae;g__Methanoperedens	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012026795.1	s__Methanoperedens sp012026795	76.4833	100	599	d__Archaea;p__Halobacteriota;c__Methanosarcinia;o__Methanosarcinales;f__Methanoperedenaceae;g__Methanoperedens	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902386085.1	s__Methanoperedens sp902386085	76.1559	50	599	d__Archaea;p__Halobacteriota;c__Methanosarcinia;o__Methanosarcinales;f__Methanoperedenaceae;g__Methanoperedens	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-27 20:07:07,953] [INFO] GTDB search result was written to GCA_026552815.1_ASM2655281v1_genomic.fna/result_gtdb.tsv
[2023-06-27 20:07:07,954] [INFO] ===== GTDB Search completed =====
[2023-06-27 20:07:07,958] [INFO] DFAST_QC result json was written to GCA_026552815.1_ASM2655281v1_genomic.fna/dqc_result.json
[2023-06-27 20:07:07,958] [INFO] DFAST_QC completed!
[2023-06-27 20:07:07,958] [INFO] Total running time: 0h0m35s